6DQU

Crystal structure of Haemophilus influenzae OppA complex with GIINTL


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2950.1M sodium acetate pH 4.6, 2.1M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
1.9938.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.895α = 90
b = 92.956β = 90
c = 108.335γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2018-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.0781APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6535.8899.90.05916.9958988
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.90.58939.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6535.8856057286299.820.1620.15980.2069RANDOM31.322
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
4.2-1.58-2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_3_deg13.898
r_dihedral_angle_4_deg9.249
r_dihedral_angle_1_deg5.897
r_angle_refined_deg1.695
r_angle_other_deg0.864
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.34
r_dihedral_angle_3_deg13.898
r_dihedral_angle_4_deg9.249
r_dihedral_angle_1_deg5.897
r_angle_refined_deg1.695
r_angle_other_deg0.864
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4159
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms5

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BALBESphasing
ARP/wARPmodel building